2cdq

Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S- adenosylmethionine

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ASPARTOKINASE

ARABIDOPSIS THALIANA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	LYSINE × 4 D(-)-TARTARIC ACID × 2 S-ADENOSYLMETHIONINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9LYU8_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–510； UniProt 61–569 Author chain B； PDBConstruct 2–510； UniProt 61–569

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2cdq
Deposition date deposition_date	2006-01-26
Structure title title	Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S- adenosylmethionine
Keywords keywords	;ASPARTATE KINASE, AMINO ACID METABOLISM, ACT DOMAIN, ALLOSTERY, S-ADENOSYLMETHIONINE, LYSINE, ALLOSTERIC EFFECTOR, PLANT, TRANSFERASE, AMINO ACID BIOSYNTHESIS ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2cdq__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2cdq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2cdq__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.47 Å
Rg (electron density)	34.27 Å
Total Rg	34.66 Å
Atom count	7346
Residues	940
Excluded volume	132660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2cdq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	ASPARTOKINASE
Molecular weight formula_weight	55960.3 kDa
EC 编号 ec_number	2.7.2.4
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7522

MGSRNIVRAVLEEKKTEAITEVDEKGITCVMKFGGSSVASAERMKEVADLILTFPEESPVIVLSAMGKTTNNLLLAGEKAVSCGVSNASEIEELSIIKELHIRTVKELNIDPSVILTYLEELEQLLKGIAMMKELTLRTRDYLVSFGECLSTRIFAAYLNTIGVKARQYDAFEIGFITTDDFTNGDILEATYPAVAKRLYDDWMHDPAVPIVTGFLGKGWKTGAVTTLGRGGSDLTATTIGKALGLKEIQVWKDVDGVLTCDPTIYKRATPVPYLTFDEAAELAYFGAQVLHPQSMRPAREGEIPVRVKNSYNPKAPGTIITKTRDMTKSILTSIVLKRNVTMLDIASTRMLGQVGFLAKVFSIFEELGISVDVVATSEVSISLTLDPSKLWSRELIQQELDHVVEELEKIAVVNLLKGRAIISLIGNVQHSSLILERAFHVLYTKGVNVQMISQGASKVNISFIVNEAEAEGCVQALHKSFFESGDLSELLIQPRLGNGSPVRTLQVEN

Source Source

Source organism organism	ARABIDOPSIS THALIANA
Common name common_name	MOUSE-EAR CRESS
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	LYSINE
Molecular weight formula_weight	147.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	D(-)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2cdqa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d2cdqa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.10 — Aspartokinase allosteric domain-like

Domain ID domain_id	d2cdqa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.10 — Aspartokinase allosteric domain-like

Domain ID domain_id	d2cdqb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.73 — Carbamate kinase-like
Superfamily Superfamily superfamily	c.73.1 — Carbamate kinase-like
Family Family family	c.73.1.3 — PyrH-like

Domain ID domain_id	d2cdqb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.10 — Aspartokinase allosteric domain-like

Domain ID domain_id	d2cdqb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.10 — Aspartokinase allosteric domain-like

CATH v4.4 (8 domains)

Domain ID domain_id	2cdqA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	2cdqA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1320 — Aspartokinase, catalytic domain

Domain ID domain_id	2cdqA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	260 — ACT domain

Domain ID domain_id	2cdqA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	260 — ACT domain

Domain ID domain_id	2cdqB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1160 — Carbamate kinase
Homologous superfamily homologous superfamily	10 — Acetylglutamate kinase-like

Domain ID domain_id	2cdqB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1320 — Aspartokinase, catalytic domain

Domain ID domain_id	2cdqB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	260 — ACT domain

Domain ID domain_id	2cdqB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	260 — ACT domain

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Unit-cell length a length_a	117.342 Å
Unit-cell length b length_b	117.342 Å
Unit-cell length c length_c	255.283 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	15.670 Å
R factor r_factor	0.2040
R_work r_work	0.2020
R_free r_free	0.2440

Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S- adenosylmethionine

1. Protein Identity and Related Structures Protein Identity & Related Structures

ASPARTOKINASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2cdq__assembly_1__model_1

2cdq__assembly_1__model_1 | I(q)

2cdq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of Arabidopsis thaliana aspartate kinase complexed with lysine and S- adenosylmethionine

1. Protein Identity and Related Structures Protein Identity & Related Structures

ASPARTOKINASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2cdq__assembly_1__model_1

2cdq__assembly_1__model_1 | I(q)

2cdq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)